Hello -
Can you provide some example code?
Any protein ambiguity should map to X. Unlike DNA which has lots of
ambiguity codes with different meanings. BioJava can support all kinds of
protein ambiguity but when they are tokenized they should all end up as X.
- Mark
"Tal Blum" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
07/24/2005 10:14 AM
To: <biojava-l@biojava.org>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Protein CharacterTokenization
Hi,
There is something strange with the protein alphabet
CharacterTokenization.
It knows how to parse the ambiguity symbol 'X', but it does not contain
the
other way around mapping of the protein alphabet ambiguity symbol to 'X'.
Is
that the way it should be or is that a bug?
Can someone suggest a way I can correct it? The Alphabet is wrapped in a
WellKnownTokenizationWrapper in AlphabetManager, so I can't simply add a
Symbol to it.
Thanks, tal
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